MOTIVATION The growing interest in the role of stochasticity in biochemical systems drives the demand for tools to analyse stochastic dynamical models of chemical reactions. One powerful tool to elucidate performance of dynamical systems is sensitivity analysis. Traditionally, however, the concept of sensitivity has mainly been applied to deterministic systems, and the difficulty to generalize these concepts for stochastic systems results from necessity of extensive Monte Carlo simulations. RESULTS Here we present a Matlab package, StochSens, that implements sensitivity analysis for stochastic chemical systems using the concept of the Fisher Information Matrix (FIM). It uses the linear noise approximation to represent the FIM in terms of solutions of ordinary differential equations. This is the first computational tool that allows for quick computation of the Information Matrix for stochastic systems without the need for Monte Carlo simulations. AVAILABILITY http://www.theosysbio.bio.ic.ac.uk/resources/stns SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.